Alignments for a candidate for deoA in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Amycolatopsis halophila YIM 93223

Align Pyrimidine-nucleoside phosphorylase; PYNP; Py-NPase; EC 2.4.2.2 (characterized)
to candidate WP_084037139.1 AMYHA_RS12540 thymidine phosphorylase

Query= SwissProt::P77836
         (433 letters)



>NCBI__GCF_000504245.1:WP_084037139.1
          Length = 446

 Score =  345 bits (884), Expect = 2e-99
 Identities = 205/430 (47%), Positives = 265/430 (61%), Gaps = 13/430 (3%)

Query: 4   VDLIEKKRDGHALTKEEIQFIIEGYTKGDIPDYQMSALAMAIFFRGMNEEETAELTMAMV 63
           VD+I  KRDG  L  E I ++++ YTKG + + QM+ALAMAI   GM+  ETA  T AM+
Sbjct: 27  VDIIGAKRDGAPLPGEWIDWVVDAYTKGMVTEAQMAALAMAIRIHGMDSAETAHWTTAMI 86

Query: 64  HSGDTIDLSRIEGIKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDK 123
            SG+ + L  ++   VDKHSTGGVGD  TLVL PLVA+ G  V ++SGRGLGHTGGT+DK
Sbjct: 87  DSGERLWLP-VDRPTVDKHSTGGVGDKVTLVLAPLVAACGAAVPQLSGRGLGHTGGTLDK 145

Query: 124 LESVPGFHVEITNDEFIDLVNKNKIAVVGQSGNLTPADKKLYALRDVTATVNSIPLIASS 183
           LES+PG+   ++  E I  +   +  V   S  L PAD+KLYALRDVTATV SIPLIASS
Sbjct: 146 LESIPGWRANLSTAEMISQLTNIRAVVAAASTALAPADRKLYALRDVTATVESIPLIASS 205

Query: 184 IMSKKIAAGADAIVLDVKTGVGAFMKDLNDAKALAKAMVDIGNRVGRKTMAIISDMSQPL 243
           IMSKKIAAG  ++VLDVK G GAFMK    A  LA+ MV+IG   G  T A+++DM+ PL
Sbjct: 206 IMSKKIAAGPQSLVLDVKVGSGAFMKSREQAAELAQTMVEIGRSHGVATTALLTDMATPL 265

Query: 244 GYAIGNALEVKEAIDTLKGEGPEDFQELCLVLGSHMVYLAEKASSLEEARHMLEKAMKDG 303
           G   GNA+EV EA+D L+G GP+D  EL L L   M++LA     L +    LE  +  G
Sbjct: 266 GRTAGNAVEVAEAVDVLRGAGPDDVVELTLTLAREMLHLA----GLPDVD--LEPILASG 319

Query: 304 SALQTFKTFLAAQGGDASVVDDPSKLPQAKYIIELEAKEDGYVSEIVADAVGTAAMWLGA 363
            A + +   + AQGGD       + LP  K+I  LEA +DG VSE+ A AVG +A  LGA
Sbjct: 320 QAYEVWCKMIRAQGGDPD-----APLPSPKHIHVLEADDDGIVSEMDALAVGISAWRLGA 374

Query: 364 GRATKESTIDLAVGLVLRKKVGDAVKKGESLVTIYSNR-EQVDDVKQKLYENIRISATPV 422
           GR    +T+  A G+ L    GD +  G+ L  ++++  + V      L   I IS TP 
Sbjct: 375 GRIAPGATVQHAAGVRLLVTEGDRISSGQPLAELHTDTPDAVPAAVSALSAGIVISKTPP 434

Query: 423 QAPTLIYDKI 432
               L+ D I
Sbjct: 435 TRRPLVIDVI 444


Lambda     K      H
   0.315    0.133    0.361 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 480
Number of extensions: 23
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 433
Length of database: 446
Length adjustment: 32
Effective length of query: 401
Effective length of database: 414
Effective search space:   166014
Effective search space used:   166014
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)

Align candidate WP_084037139.1 AMYHA_RS12540 (thymidine phosphorylase)
to HMM TIGR02644 (pdp: pyrimidine-nucleoside phosphorylase (EC 2.4.2.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR02644.hmm
# target sequence database:        /tmp/gapView.1278301.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02644  [M=417]
Accession:   TIGR02644
Description: Y_phosphoryl: pyrimidine-nucleoside phosphorylase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-160  520.3   0.0     2e-160  520.1   0.0    1.0  1  NCBI__GCF_000504245.1:WP_084037139.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_084037139.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.1   0.0    2e-160    2e-160       2     416 ..      27     429 ..      26     430 .. 0.98

  Alignments for each domain:
  == domain 1  score: 520.1 bits;  conditional E-value: 2e-160
                             TIGR02644   2 veiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldlselkk 74 
                                           v+ii  Krdg  l  e i++++++ytkg +++ Q++al+mai ++g+d++Et+++T+am++sGe+l +  +++
  NCBI__GCF_000504245.1:WP_084037139.1  27 VDIIGAKRDGAPLPGEWIDWVVDAYTKGMVTEAQMAALAMAIRIHGMDSAETAHWTTAMIDSGERL-WLPVDR 98 
                                           89***************************************************************9.6679** PP

                             TIGR02644  75 ikvDKHStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefieivkkvgla 147
                                           ++vDKHStGGvGDkv+LvlaPlvaa+g++v++lSGRgLghTGGTlDKLesipG++++ls++e+i++++++ ++
  NCBI__GCF_000504245.1:WP_084037139.1  99 PTVDKHSTGGVGDKVTLVLAPLVAACGAAVPQLSGRGLGHTGGTLDKLESIPGWRANLSTAEMISQLTNIRAV 171
                                           ************************************************************************* PP

                             TIGR02644 148 iigqtkdlapaDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmktleeakeLakelv 220
                                           ++++++ lapaD+klYalRdvt+Tv+s+pLiasSi+sKK+aag ++lvlDvkvG+GaFmk+ e+a eLa+++v
  NCBI__GCF_000504245.1:WP_084037139.1 172 VAAASTALAPADRKLYALRDVTATVESIPLIASSIMSKKIAAGPQSLVLDVKVGSGAFMKSREQAAELAQTMV 244
                                           ************************************************************************* PP

                             TIGR02644 221 eigkkagrkvvalltdmnepLgkaiGNalEvkeavevLkgegpadlkelvlalaaemlllaklakteeeakek 293
                                           eig+++g+ ++alltdm +pLg+++GNa+Ev+eav+vL+g gp d++el+l+la+eml la+l +       +
  NCBI__GCF_000504245.1:WP_084037139.1 245 EIGRSHGVATTALLTDMATPLGRTAGNAVEVAEAVDVLRGAGPDDVVELTLTLAREMLHLAGLPD------VD 311
                                           ***************************************************************98......78 PP

                             TIGR02644 294 leevlesgkalekfkefveaqgGdlevlkeekklakakkkeevkaeksgvieeidaeelgliavelgaGRakk 366
                                           le +l+sg+a+e ++++++aqgGd+     ++ l+++k+ + ++a+ +g+++e+da ++g+ a++lgaGR   
  NCBI__GCF_000504245.1:WP_084037139.1 312 LEPILASGQAYEVWCKMIRAQGGDP-----DAPLPSPKHIHVLEADDDGIVSEMDALAVGISAWRLGAGRIAP 379
                                           99**********************7.....689**************************************** PP

                             TIGR02644 367 edkidleaGielekkvgdkvkkgdllltlyssdeekaeeaakalkkaiki 416
                                             +++++aG+ l + +gd++++g++l++l++++++ + +a +al++ i i
  NCBI__GCF_000504245.1:WP_084037139.1 380 GATVQHAAGVRLLVTEGDRISSGQPLAELHTDTPDAVPAAVSALSAGIVI 429
                                           ************************************99999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (446 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.55
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources